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- PDB-1yd9: 1.6A Crystal Structure of the Non-Histone Domain of the Histone V... -

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Basic information

Entry
Database: PDB / ID: 1yd9
Title1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MacroH2A1.1.
ComponentsCore histone macro-H2A.1
KeywordsSTRUCTURAL PROTEIN / Alpha-Beta Structure / A1pp Domain / Macro-Domain
Function / homology
Function and homology information


: / : / : / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress / regulation of response to oxidative stress / Barr body ...: / : / : / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress / regulation of response to oxidative stress / Barr body / heterochromatin formation => GO:0031507 / sex-chromosome dosage compensation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / establishment of protein localization to chromatin / positive regulation of endodermal cell differentiation / double-stranded methylated DNA binding / rDNA binding / negative regulation of protein serine/threonine kinase activity / protein serine/threonine kinase inhibitor activity / positive regulation of keratinocyte differentiation / nucleosomal DNA binding / negative regulation of gene expression, epigenetic / nuclear chromosome / regulation of lipid metabolic process / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / epigenetic regulation of gene expression / condensed chromosome / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / nucleosome assembly / nucleosome / transcription cis-regulatory region binding / protein heterodimerization activity / chromatin binding / chromatin / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 ...Core histone macro-H2A / Core histone macro-H2A, macro domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Core histone macro-H2A.1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsChakravarthy, S. / Swamy, G.Y.S.K. / Caron, C. / Perche, P.Y. / Pehrson, J.R. / Khochbin, S. / Luger, K.
CitationJournal: Mol.Cell.Biol. / Year: 2005
Title: Structural characterization of the histone variant macroH2A
Authors: Chakravarthy, S. / Gundimella, S.K. / Caron, C. / Perche, P.Y. / Pehrson, J.R. / Khochbin, S. / Luger, K.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The first five residues GPLGS are cloning artifacts. The sequence 6-51 is variance ...SEQUENCE The first five residues GPLGS are cloning artifacts. The sequence 6-51 is variance splicing in isoform 1.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core histone macro-H2A.1
B: Core histone macro-H2A.1
C: Core histone macro-H2A.1
D: Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9428
Polymers82,1544
Non-polymers7884
Water9,728540
1
A: Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7352
Polymers20,5391
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7352
Polymers20,5391
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7352
Polymers20,5391
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7352
Polymers20,5391
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.114, 89.791, 95.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Core histone macro-H2A.1 / Histone macroH2A1 / mH2A1 / H2A.y / H2A/y


Mass: 20538.521 Da / Num. of mol.: 4 / Fragment: Non-Histone Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: H2afy / Production host: Escherichia coli (E. coli) / References: UniProt: Q02874
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1726
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2921vapor diffusion, sitting drop5.928% PEG 2000, 0.2M Ammonium Sulphate, 0.1M Sodium Acetate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K
2922vapor diffusion, sitting drop5.928% PEG 2000, 0.2M Ammonium Sulphate, 0.1M Sodium Acetate, Potassium Dicyanoaurate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.074853
SYNCHROTRONALS 8.3.121.074800, 1.039990
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 25, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0748531
21.07481
31.039991
ReflectionResolution: 1.6→50 Å / Num. all: 94878 / Num. obs: 91017 / % possible obs: 96 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.67 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 2757 Random
Rwork0.235 --
all-94878 -
obs-91017 -
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5629 0 4 540 6173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_deg1.2613

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